Can't get script to auto execute
I had the same problem and got my answer here: https://blender.stackexchange.com/a/84392/38217

Note that this executes on ANY Blender File you open, but maybe it will suffice.

import bpy
import sys

@bpy.app.handlers.persistent
def setup_path(*args):
    sys.path.append('/Path/To/My/Blender/Project')
bpy.app.handlers.load_post.append(setup_path)
setup_path()



  Put this code into a Python file and place it into
  ~/.config/blender/2.78/scrips/startup/setup-path.py (replace
  ~/config/blender with %APPDATA%/Blender Foundation/Blender on Windows,
  and something along those lines on MacOS).